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Structure of pectate lyase II from xanthomonas campestris pv. campestris str. atcc 33913

Analyse Structure of pectate lyase II from xanthomonas campestris pv. campestris str.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QX3
Type: protein
Length: 660 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pectate lyase II
EC: 4.2.2.2
UniProt: Q8P6Z9
Ligands: PO4
Pockets: 3 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pectate lyase II (EC 4.2.2.2)	protein	330	10% helix, 38% strand	Q8P6Z9

Ligands and binding sites

PO4 · Phosphate ion · ion · 5 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1049	0.76	0.78	80	empty
2	66	0.30	0.74	12	PO4
3	61	0.28	0.73	15	PO4

Interfaces

1 interface between chains.

A–B · 949 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2QX3 · Structure of pectate lyase II from Xanthomonas campestris pv. campestris str. ATCC 33913 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q8P6Z9
Elsewhere: RCSB PDB 2QX3 · PDBe 2QX3 · UniProt Q8P6Z9

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